knitr::opts_chunk$set(echo = FALSE, message = FALSE)
library(Seurat)
library(ggplot2)
library(data.table)
library(MAST)
library(SingleR)
library(dplyr)
library(tidyr)
library(limma)
library(scRNAseq)## Warning: Using `as.character()` on a quosure is deprecated as of rlang 0.3.0.
## Please use `as_label()` or `as_name()` instead.
## This warning is displayed once per session.
Things that were brought up last meeting:
What are the MEP/Mast cells, are these really MEPs?
## Warning in FetchData(object = object, vars = features, cells = cells): The
## following requested variables were not found: Ahspp
## Warning in FetchData(object = object, vars = features, cells = cells): The
## following requested variables were not found: C3orf58
## Warning in FetchData(object = object, vars = features, cells = cells): The
## following requested variables were not found: C6orf25
Other markers that I have from priya and other sources.
Neither of these was useful
Looking at some of the top hits (Mcpt8, Prss34) and other MEP genes (Gata2, Runx1, Cpa3), to see how they overlap
##
## Itga2b = 0 Itga2b > 0
## Mcpt8 = 0 3 6
## Mcpt8 > 0 39 544
##
## Itga2b = 0 Itga2b > 0
## Prss34 = 0 11 18
## Prss34 > 0 31 532
##
## Itga2b = 0 Itga2b > 0
## Gata2 = 0 4 3
## Gata2 > 0 38 547
##
## Itga2b = 0 Itga2b > 0
## Runx1 = 0 10 8
## Runx1 > 0 32 542
##
## Itga2b = 0 Itga2b > 0
## Cpa3 = 0 12 125
## Cpa3 > 0 30 425
##
## Mcpt8 = 0 Mcpt8 > 0
## Prss34 = 0 8 21
## Prss34 > 0 1 562
##
## Mcpt8 = 0 Mcpt8 > 0
## Gata2 = 0 2 5
## Gata2 > 0 7 578
##
## Mcpt8 = 0 Mcpt8 > 0
## Runx1 = 0 5 13
## Runx1 > 0 4 570
##
## Mcpt8 = 0 Mcpt8 > 0
## Cpa3 = 0 2 135
## Cpa3 > 0 7 448
##
## Prss34 = 0 Prss34 > 0
## Gata2 = 0 3 4
## Gata2 > 0 26 559
##
## Prss34 = 0 Prss34 > 0
## Runx1 = 0 9 9
## Runx1 > 0 20 554
##
## Prss34 = 0 Prss34 > 0
## Cpa3 = 0 5 132
## Cpa3 > 0 24 431
##
## Gata2 = 0 Gata2 > 0
## Runx1 = 0 4 14
## Runx1 > 0 3 571
##
## Gata2 = 0 Gata2 > 0
## Cpa3 = 0 6 131
## Cpa3 > 0 1 454
##
## Runx1 = 0 Runx1 > 0
## Cpa3 = 0 8 129
## Cpa3 > 0 10 445
Most of these cells are coming from the enriched Mpl experiment so I would start there.
## p_val avg_logFC pct.1 pct.2 p_val_adj
## Cd200r3 1.222623e-253 2.382079 0.990 0.032 2.214293e-249
## Cyp11a1 1.060851e-252 2.902921 0.998 0.049 1.921307e-248
## Gata2 1.018616e-244 2.346238 0.990 0.070 1.844815e-240
## Cd200r4 7.162088e-242 1.849539 0.980 0.059 1.297126e-237
## Il1rl1 7.425986e-240 2.046625 0.972 0.050 1.344920e-235
## Padi2 5.276162e-239 1.809938 0.968 0.045 9.555657e-235